MEX vs Matlab in ANN?

I am running ANN in Matlab software and the calculation is based on Matlab algorithm. I have million data points and each run on my PC takes about 5 hours (icore5). Recently, I am using a new laptop (icore7) and the default is based on MEX algorithm and each run takes some minutes. I am worried that the algorithm's result are different. I have no idea what is different b/w these two algorithms?

[James Tursa]

Do you have side-by-side run results that are significantly different? Or are you just worried that they might be different because of the speed difference? Mex routines can run significantly faster than m-file routines, but it all depends on what exactly the m-file and mex routine are doing.